R Reference Card
R Reference Card by Tom Short EPRI PEAC
psych: Procedures for Psychological Psychometric
https://cran.r-project.org/web/packages/psych/psych.pdf
metafor: Meta-Analysis Package for R
26?/08?/2022 Network meta- ... package website: https://www.metafor-project.org ... See also Morris and DeShon (2002) for a thorough discussion of the ...
An Introduction to R
CRAN family of Internet sites (via https://CRAN.R-project.org) and elsewhere. More details on packages are given later (see Chapter 13 [Packages] page 77).
R pour les débutants
site internet du Comprehensive R Archive Network (CRAN)5 o`u se trouvent aussi les instructions `a suivre 3http://cran.r-project.org/doc/FAQ/R-FAQ.html.
R for Beginners
distributed from the internet site of the Comprehensive R Archive Network. (CRAN)5 where the instructions 3http://cran.r-project.org/doc/FAQ/R-FAQ.html.
rpart.pdf
https://cran.r-project.org/package=rpart. BugReports https://github.com/bethatkinson/rpart/issues. Date/Publication 2022-01-24 20:12:45 UTC.
adespatial: Multivariate Multiscale Spatial Analysis
02?/09?/2022 See https://en.wikipedia.org/wiki/Universal_Transverse_Mercator_coordinate_system. Value. A matrix with n rows containing a set of k ...
randomForest: Breiman and Cutlers Random Forests for
URL https://www.stat.berkeley.edu/~breiman/RandomForests/. NeedsCompilation yes. Repository CRAN. Date/Publication 2022-05-23 08:27:49 UTC. R topics
atable: Create Tables for Reporting Clinical Trials
BugReports https://github.com/arminstroebel/atable/issues. NeedsCompilation no. Repository CRAN. Date/Publication 2022-02-21 09:00:21 UTC. R topics
The Comprehensive R Archive Network - ISM
R is very much a vehicle for newly developing methods of interactive data analysis It has developed rapidly and has been extended by a large collection of packages However most programs written in R are essentially ephemeral written for a single piece of data analysis 1 2 Related software and documentation
What are R and Cran (•• )?
What are R ??? and CRAN ???? (´•?•`)? R is ‘GGNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.
Where can I find Cran data?
CRAN is covered by Thomson Reuters Data Citation Index. CRAN is covered by SCOPUS. Data is available under GNU license. Mirror sites can be found here https://cran.r-project.org/mirrors.html .
How do I submit a package to Cran?
To “submit” a package to CRAN, check that your submission meets the CRAN Repository Policy and then use the web form . If this fails, send an email to CRAN-submissions@R-project.org following the policy. Please do not attach submissions to emails, because this will clutter up the mailboxes of half a dozen people.
How many R packages are there?
SeeSection “R packages” inR FAQ, for a complete list. There are thousands of contributed packages for R, written by many different authors. Someof these packages implement specialized statistical methods, others give access to data or hard-ware, and others are designed to complement textbooks.
RforBeginners
EmmanuelParadis
InstitutdesSciencesdel'Evolution
UniversiteMontpellierII
F-34095Montpelliercedex05
France
E-mail:paradis@isem.univ-montp2.fr
c copyrightnoticeisincluded.Contents
1Preamble1
2Afewconceptsbeforestarting3
3DatawithR9
4GraphicswithR36
5StatisticalanalyseswithR55
6ProgrammingwithRinpratice64
7LiteratureonR71
1Preamble
details,sometimeswithtables. andRobertGentleman2.Thereareimportant
3,acopy
ofwhichisalsodistributedwithR. 4; astheRDevelopmentCoreTeam. (CRAN) analyses. 2See 34Formoreinformation:http://www.gnu.org/
5http://cran.r-project.org/
1 ableontheinternet exibility.Whereas exibility6Forexample:http://stat.cmu.edu/S/
22Afewconceptsbeforestarting
Weshallseerstbrie
yhowRworks.Then,Iwilldescribethe\assign"2.1HowRworks
so.25).AnR
functionmaybesketchedasfollows: arguments! options! function defaultarguments =)result 367).The
thecomputer:notemporarylesareused(Fig.1).Thereadingsandwritings
fromaremoteserverthroughinternet. functionsandoperators \data"objects ?6)XXXXXXXz \results"objects.../library/base/ /stast/ /graphics/ ...libraryof functions data les internetPSJPEG...keyboard
mouse -commands screenActivememoryHarddisk
Figure1:AschematicviewofhowRworks.
thediskinadirectorycalledRHOME/library(RHOMEisthedirectory
leR package. >n [1]10 4 ).Rdiscriminates orthereverse: >n<-15 >n [1]15 >5->n >n [1]5 >x<-1 >X<-10 >x [1]1 >X [1]10 >n<-10+2 >n [1]12 >n<-3+rnorm(1) >n [1]2.208807 andvarianceunity(p.17).Notethatyoucansimplytypeanexpression
screenbutisnotstoredinmemory: >(10+2)*5 [1]60 5 derstanding. objectsaredisplayed. >name<-"Carmen";n1<-10;n2<-100;m<-0.5 >ls() [1]"m""n1""n2""name" used: >ls(pat="m") [1]"m""name" >ls(pat="^m") [1]"m" >ls.str() m:num0.5 n1:num10 n2:num100 name:chr"Carmen" detailswiththeoptionmax.level=-1: >M<-data.frame(n1,n2,m) >ls.str(pat="M")M:`data.frame':1obs.of3variables:
$n1:num10 $n2:num100 $m:num0.5 >ls.str(pat="M",max.level=-1)M:`data.frame':1obs.of3variables:
62.3Theon-linehelp
>?lmError:syntaxerror
>help("*")Arithmeticpackage:baseRDocumentation
ArithmeticOperators
bysectionswhichgivedetailedinformation.Description:briefdescription.
thetypicaluse.Details:detaileddescription.
ator. thehelpwiththefunctionexample. 7 >help("bs") youcouldtry'help.search("bs")' >help("bs",try.all.packages=TRUE) canbefoundinthefollowingpackages:PackageLibrary
splines/usr/lib/R/library theoptionpackage: >help("bs",package="splines") bspackage:splinesRDocumentationB-SplineBasisforPolynomialSplines
Description:
>help.start() =TRUE)). >apropos(help) [1]"help"".helpForCall""help.search" [4]"help.start" 83DatawithR
3.1Objects
dependsontheattributesofthelatter. numeric,character,complex >x<-1 >mode(x) [1]"numeric" >length(x) [1]1 >A<-"Gomphotherium";compar<-TRUE;z<-1i >mode(A);mode(compar);mode(z) [1]"character" [1]"logical" [1]"complex" >N<-2.1e23 >N [1]2.1e+23 9 >x<-5/0 >x [1]Inf >exp(x) [1]Inf >exp(-x) [1]0 >x-x [1]NaN 14, theoptionqmethodofthisfunction). >x [1]"Doublequotes\"delimitateR'sstrings." >cat(x)Doublequotes"delimitateR'sstrings.
slashes(butsinglequotesmustbe!): >x [1]"Doublequotes\"delimitateR'sstrings." data. objectmodesseveralmodes possibleinthe sameobject? factornumericorcharacterNo tsnumeric,character,complexorlogicalNo function,expression,... 10 object,includedlists!3.2Readingdatainale
directory. 8 restrictheretoreadinglesinASCIIformat. nameddata.dat,thecommand: >mydata<-read.table("data.dat") mydata[,1],mydata[,2],...9Thereareseveraloptionswhosedefault
thefollowingtable: adataframe.Wewillseelater(p.18)somedetailsonmanipulatingobjects.
11 colClasses=NA,nrows=-1, strip.white=FALSE,blank.lines.skip=TRUE, comment.char="#") typeURL(http://...) thevariablesonitsrstline tabulation decthecharacterusedforthedecimalpoint le(bydefault:1,2,3,...) columns \blanks"areadded thecharactervariables comment.char="") values: fill=TRUE,...) fill=TRUE,...) fill=TRUE,...) fill=TRUE,...) 12Thefunctionscanismore
exiblethanread.table.Adierenceisthat quote=if(sep=="\n")""else"'\"",dec=".", skip=0,nlines=0,na.strings="NA", allowEscapes=TRUE) blankline) septheeldseparatorusedinthele decthecharacterusedforthedecimalpoint nlinesthenumberoflinestoread datale) \blanks"areadded thecharactervariables beenread blank.lines.skipifTRUE,ignoresblanklines onasinglelineinthele(FALSE) fault)orreadasverbatim 13 widthformat: as.is=FALSE,skip=0,row.names,col.names, n=-1,buffersize=2000,...) ceptwidthswhichspeciesthewidthoftheelds withthefollowingcommand:A1.501.2
A1.551.3
B1.601.4
B1.651.5
C1.701.6
C1.751.7
>mydataV1V2V3
1A1.501.2
2A1.551.3
3B1.601.4
4B1.651.5
5C1.701.6
6C1.751.7
3.3Savingdata
andoptionsare: eol="\n",na="NA",dec=".",row.names=TRUE, xthenameoftheobjecttobewritten septheeldseparatorusedinthele nathecharactertobeusedformissingdata decthecharacterusedforthedecimalpoint col.namesid.forthenamesofthecolumns byn",if"d"each"isreplacedby"" 14 thelealreadyexists(FALSE,thedefault). =ls(all=TRUE),file=".RData").3.4Generatingdata
3.4.1Regularsequences
with: >x<-1:30 arithmeticoperatorswithinanexpression: >1:10-1 [1]0123456789 >1:(10-1) [1]123456789 >seq(1,5,0.5) [1]1.01.52.02.53.03.54.04.55.0Onecanusealso:
>seq(length=9,from=1,to=5) [1]1.01.52.02.53.03.54.04.55.0 >c(1,1.5,2,2.5,3,3.5,4,4.5,5) [1]1.01.52.02.53.03.54.04.55.0 15 >z<-scan()1:1.01.52.02.53.03.54.04.55.0
10:Read9items
>z [1]1.01.52.02.53.03.54.04.55.0 >rep(1,30) [1]111111111111111111111111111111 bythenumbersgivenasarguments: >sequence(4:5) [1]123412345 >sequence(c(10,5)) [1]1234567891012345 >gl(3,5) [1]111112222233333Levels:123
>gl(3,5,length=30) [1]111112222233333111112222233333Levels:123
>gl(2,6,label=c("Male","Female")) [1]MaleMaleMaleMaleMaleMale [7]FemaleFemaleFemaleFemaleFemaleFemaleLevels:MaleFemale
>gl(2,10) [1]11111111112222222222Levels:12
>gl(2,1,length=20) [1]12121212121212121212Levels:12
>gl(2,2,length=20) [1]11221122112211221122Levels:12
16 torsorfactorsgivenasarguments: hwsex160100Male
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